Last updated: 2019-03-01

Checks: 4 2

Knit directory: DNASeq/

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Environment: objects present

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The following objects were defined in the global environment when these results were created:

Name Class Size
a packageIQR 2.3 Kb
alignMerge cwlStepParam 306.3 Kb
bwa cwlParam 25.2 Kb
bwaAlign cwlStepParam 125.7 Kb
dats packageIQR 2.3 Kb
f1 InputParam 2.8 Kb
f2 InputParam 2.8 Kb
f3 InputParam 2.8 Kb
fastqc cwlParam 13.8 Kb
featureCounts cwlParam 19.4 Kb
fq2ubamJson cwlParam 37.4 Kb
GAlign cwlStepParam 211.9 Kb
geneBody_coverage cwlParam 21.8 Kb
genePredToBed cwlParam 16.5 Kb
gtfToGenePred cwlParam 16.5 Kb
hapCall cwlStepParam 29.6 Kb
hapJson cwlParam 19.3 Kb
jdCall cwlStepParam 129.5 Kb
jdJson cwlParam 28.3 Kb
markdup cwlParam 21.8 Kb
mc3 cwlStepParam 90.6 Kb
mergeBam cwlParam 18.4 Kb
mergeBamDup cwlStepParam 122.7 Kb
mvOut cwlParam 13.4 Kb
o1 OutputParam 2.3 Kb
o2 OutputParam 2.3 Kb
o2a OutputParam 2.3 Kb
o2b OutputParam 2.3 Kb
o2c OutputParam 2.3 Kb
o3 OutputParam 2.3 Kb
o4 OutputParam 2.4 Kb
o5 OutputParam 2.4 Kb
o6 OutputParam 2.4 Kb
o7 OutputParam 2.3 Kb
o8 OutputParam 2.3 Kb
p1 InputParam 2.8 Kb
p10 InputParam 2.8 Kb
p11 InputParam 2.8 Kb
p12 InputParam 2.8 Kb
p13 InputParam 2.8 Kb
p2 InputParam 2.8 Kb
p3 InputParam 2.8 Kb
p4 InputParam 2.8 Kb
p5 InputParam 2.8 Kb
p6 InputParam 2.8 Kb
p7 InputParam 2.8 Kb
p8 InputParam 2.8 Kb
p9 InputParam 2.8 Kb
read_distribution cwlParam 16.6 Kb
req1 list 416 bytes
req2 list 416 bytes
req3 list 416 bytes
rnaseq_Sf cwlStepParam 315.6 Kb
rscripts character 816 bytes
RSeQC cwlStepParam 126 Kb
runWDL cwlParam 21.7 Kb
s1 stepParam 19.5 Kb
s2 stepParam 44.2 Kb
s3 stepParam 20.1 Kb
s4 stepParam 19.5 Kb
s5 stepParam 28.1 Kb
s6 stepParam 133.4 Kb
sam2bam cwlParam 13.9 Kb
samtools_flagstat cwlParam 13.8 Kb
samtools_index cwlParam 14.4 Kb
sortBam cwlParam 13.8 Kb
STAR cwlParam 32.2 Kb
ubam2bamJson cwlParam 16.6 Kb

Seed: set.seed(20181205)

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Untracked files:
    Untracked:  analysis/Rcwl_DNASeq_Align.Rmd
    Untracked:  analysis/Rcwl_DNASeq_Align.Rmd~
    Untracked:  analysis/Rcwl_GATK4.Rmd
    Untracked:  analysis/Rcwl_GATK4.Rmd~
    Untracked:  analysis/Rcwl_MC3.Rmd
    Untracked:  analysis/Rcwl_MC3.Rmd~
    Untracked:  bwaOutput.sam
    Untracked:  code/gatk.R
    Untracked:  code/gatk.R~
    Untracked:  data/fq1_1.fq
    Untracked:  data/fq1_2.fq
    Untracked:  data/fq2_1.fq
    Untracked:  data/fq2_2.fq
    Untracked:  data/normal.bam
    Untracked:  data/normal.bam.bai
    Untracked:  data/normal_1.fq
    Untracked:  data/normal_2.fq
    Untracked:  data/tumor.bam
    Untracked:  data/tumor.bam.bai
    Untracked:  data/tumor_1.fq
    Untracked:  data/tumor_2.fq
    Untracked:  file3f79542e1d70/
    Untracked:  output/BAM/
    Untracked:  output/GATK/
    Untracked:  output/interval.21.interval_list
    Untracked:  output/interval.21.intervals
    Untracked:  output/interval.list~
    Untracked:  output/interval.txt
    Untracked:  output/mc3/
    Untracked:  sample1.bam
    Untracked:  sample1.bam.bai
    Untracked:  temp/DNASeq.Rmd
    Untracked:  temp/DNASeq.Rmd~
    Untracked:  temp/analysis/filed13439812939/
    Untracked:  temp/analysis/temp/
    Untracked:  temp/data/test.1_fastq.gz
    Untracked:  temp/data/test.2_fastq.gz
    Untracked:  temp/output/BAM/
    Untracked:  test.bam
    Untracked:  tmpl1.json

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Introduction

The DNASeq alignment pipeline was included in the RcwlPipelines package. It majorly includes two steps:

  • bwa alignment by read groups.
  • Merge by samples and markduplicates.

Here is the short summary and step plots.

suppressPackageStartupMessages(library(Rcwl))
library(RcwlPipelines)
data("alignMerge")

short(alignMerge)
inputs:
- idBam
- RG
- threads
- Ref
- FQ1s
- FQ2s
outputs:
- oBam
- matrix
- Idx
- stat
steps:
- bwaAlign
- mergeBamDup
plotCWL(alignMerge)
  1. BWA alignment
plotCWL(runs(alignMerge)$bwaAlign)
  1. Merge and markduplicates
plotCWL(runs(alignMerge)$mergeBamDup)

Prepara data

Here is an example of two samples. The “sample1” have two lanes of sequences and the “sample2” only has one pair of reads. The lists of reads1 fq1, reads2 fq2, read groups and output BAM names are defined in the inputList. The reference genome and number of threads to run the job are defined in the shared options, paramList.

fq1 <- list(sample1 = list("data/fq1_1.fq", "data/fq2_1.fq"),
            sample2 = list("data/fq1_1.fq"))
fq2 <- list(sample1 = list("data/fq1_2.fq", "data/fq2_2.fq"),
            sample2 = list("data/fq1_2.fq"))
rgs <- list(sample1 = list("@RG\\tID:sample1.1\\tSM:sample1", "@RG\\tID:sample1.2\\tSM:sample1"),
            sample2 = list("@RG\\tID:sample2.1\\tSM:sample2"))
samples <- list(sample1 = "sample1.bam", sample2 = "sample2.bam")

inputList <- list(idBam = samples, RG= rgs, FQ1s = fq1, FQ2s = fq2) 
paramList <- list(threads = 2,
                  Ref = "/rpcc/bioinformatics/reference/current/hs37d5.fa")

DNA alignment pipeline

res <- runCWLBatch(alignMerge, outdir = "output/BAM",
                   inputList = inputList, paramList = paramList,
                   BPPARAM = BatchtoolsParam(workers = 2, cluster = "sge",
                                             template = "/rpcc/bioinformatics/sge.tmpl",
                                             resources = list(jobname="bwa",
                                                              threads = 2,
                                                              queue = "all.q")))

Outputs:

dir("output/BAM/sample1")
[1] "sample1.bam"          "sample1.bam.bai"      "sample1.flagstat.txt"
[4] "sample1.markdup.txt" 


sessionInfo()
R version 3.5.2 Patched (2018-12-31 r75935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)

Matrix products: default
BLAS: /home/qhu/usr/R-3.5/lib64/R/lib/libRblas.so
LAPACK: /home/qhu/usr/R-3.5/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] RcwlPipelines_0.99.0 testthat_2.0.1       BiocStyle_2.10.0    
 [4] rmarkdown_1.11       knitr_1.21           usethis_1.4.0       
 [7] devtools_2.0.1       Rcwl_0.99.14         S4Vectors_0.20.1    
[10] BiocGenerics_0.28.0  yaml_2.2.0          

loaded via a namespace (and not attached):
 [1] colorspace_1.4-0    rprojroot_1.3-2     fs_1.2.6           
 [4] rstudioapi_0.9.0    roxygen2_6.1.1      remotes_2.0.2      
 [7] xml2_1.2.0          pkgload_1.0.2       jsonlite_1.6       
[10] workflowr_1.2.0     shiny_1.2.0         DiagrammeR_1.0.0   
[13] BiocManager_1.30.4  readr_1.3.1         compiler_3.5.2     
[16] backports_1.1.3     assertthat_0.2.0    lazyeval_0.2.1     
[19] cli_1.0.1           later_0.8.0         visNetwork_2.0.5   
[22] htmltools_0.3.6     prettyunits_1.0.2   tools_3.5.2        
[25] igraph_1.2.4        gtable_0.2.0        glue_1.3.0         
[28] dplyr_0.8.0.1       batchtools_0.9.11   rappdirs_0.3.1     
[31] Rcpp_1.0.0          rgexf_0.15.3        xopen_1.0.0        
[34] debugme_1.1.0       xfun_0.5            stringr_1.4.0      
[37] ps_1.3.0            mime_0.6            XML_3.98-1.17      
[40] scales_1.0.0        hms_0.4.2           promises_1.0.1     
[43] RColorBrewer_1.1-2  memoise_1.1.0       gridExtra_2.3      
[46] ggplot2_3.1.0       downloader_0.4      rcmdcheck_1.3.2    
[49] stringi_1.3.1       highr_0.7           Rook_1.1-1         
[52] desc_1.2.0          checkmate_1.9.1     pkgbuild_1.0.2     
[55] BiocParallel_1.16.6 rlang_0.3.1         pkgconfig_2.0.2    
[58] commonmark_1.7      evaluate_0.13       purrr_0.3.0        
[61] htmlwidgets_1.3     processx_3.2.1      tidyselect_0.2.5   
[64] plyr_1.8.4          magrittr_1.5        bookdown_0.9       
[67] R6_2.4.0            base64url_1.4       pillar_1.3.1       
[70] withr_2.1.2         tibble_2.0.1        crayon_1.3.4       
[73] viridis_0.5.1       progress_1.2.0      grid_3.5.2         
[76] data.table_1.12.0   git2r_0.24.0        callr_3.1.1        
[79] influenceR_0.1.0    digest_0.6.18       xtable_1.8-3       
[82] tidyr_0.8.2         httpuv_1.4.5.1      brew_1.0-6         
[85] munsell_0.5.0       viridisLite_0.3.0   sessioninfo_1.1.1